Detection and quantification of hepatitis A virus titers from wastewater in South Africa and comparison with clinical data from the National Surveillance Database DOI Creative Commons
Kathleen Subramoney, Sipho Gwala, Emmanuel Phalane

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Abstract Wastewater surveillance is useful for monitoring the prevalence of hepatitis A virus (HAV). We developed and optimized HAV detection quantification methods wastewater samples, applied them to samples collected through a national program. Previously identified 5’-untranslated region-targeting primers probes were used develop assay. Serial dilutions HAV-positive clinical validate determine limits (LOQ). Retrospective testing weekly SARS-CoV-2 program at 26 sites in Gauteng (August 2021 March 2024) undertaken using ultrafiltration-based concentration, nucleic acids extracted KingFisher Flex purification system with isolation kit. digital PCR assay was (as genome copies/μL). Clinical data from Surveillance Database Warehouse National Health Laboratory Service compared data, epidemiological week-wise district-wise, correlations between datasets. Based on validation results, one partition (dPCR) platform equivalent an LOQ 0.4 copies/μL. In total, 2013 tested, which 349 positive (17.3%), wherein majority (304, 87.1%) had lowest concentration (2.0-2.7 gc/μL, 1-5 partitions), followed by 20 (5.7%) concentrations 2.8-3.0 gc/μL (6-10 partitions). detected 17.1% (241/1170) 26.1% correlation anti-HAV IgM detected. successfully dPCR method detect quantify determined its LOQ. Further analysis required compare facilitate appropriate interpretation results.

Language: Английский

Longitudinal wastewater-based surveillance of SARS-CoV-2 during 2023 in Ethiopia DOI Creative Commons
Daniel Abera Dinssa, Gebremedhin Gebremicael,

Yohannes Mengistu

et al.

Frontiers in Public Health, Journal Year: 2024, Volume and Issue: 12

Published: Oct. 7, 2024

Introduction Although wastewater-based epidemiology (WBE) successfully functioned as a tool for monitoring the coronavirus disease 2019 (COVID-19) pandemic globally, relatively little is known about its utility in low-income countries. This study aimed to quantify severe acute respiratory syndrome 2 (SARS-CoV-2) RNA wastewater, estimate number of infected individuals catchment areas, and correlate results with clinically reported COVID-19 cases Addis Ababa, Ethiopia. Methods A total 323 influent 33 effluent wastewater samples were collected from three Wastewater Treatment Plants (WWTPs) using 24-h composite Moore swab sampling method February November 2023. The virus was captured Ceres Nanotrap® Enhancement Reagent Microbiome Particles, then nucleic acids extracted Qiagen QIAamp Viral Mini Kit. ThermoFisher TaqPath™ kit applied perform real-time reverse transcriptase polymerase chain reaction (qRT-PCR) SARS-CoV-2 RNA. viral concentrations normalized flow rate people served. In period, spearman correlation used compare target gene concentration cases. numbers under each treatment plant calculated considering genes’ concentration, plants, gram feces per person-day, copies feces. Results detected 94% untreated samples. All ( n = 22) upflow anaerobic sludge blanket (UASB) reactor membrane bioreactor (MBR) technology SARS-COV-2 negative. contrast, two out 11 effluents Waste Stabilization Pond found positive. Positive correlations observed between weekly average cumulative Ababa. estimated Kality area 330 times during period Discussion revealed that circulating community confirmed previous reports more asymptomatic Additionally, this provides further evidence importance surveillance general monitor infectious diseases settings. Conclusion Wastewater-based can be useful tracking increment before it spreads widely throughout community.

Language: Английский

Citations

0
Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing DOI Creative Commons
Padmini Ramachandran,

Tunc Kayikcioglu,

Tamara Walsky

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

Abstract Wastewater-based analysis has emerged as a pivotal method for monitoring SARS-CoV-2 (SC2). Leveraging high-throughput sequencing on wastewater samples facilitates comprehensive, population-level assessment of circulating and emerging SC2 variants within community. This study meticulously evaluates the detection performance, variant calling accuracy, time taken from sample collection to public data release monitoring. We employed two different target enrichment panels Illumina MiSeq Oxford Nanopore Technologies (ONT) GridION platforms robust analysis. Daily routine raw grab composite took place at treatment plant (WWTP) site in Maryland, USA (MD) mid-January 2022 end June 2022. Total Nucleic Acid (TNA) was extracted executed using QIAseq DIRECT NEBNext VarSkip Short amplicon kits, with subsequent or ONT platforms, respectively. Obtained sequences analyzed our custom CFSAN Wastewater Analysis Pipeline (C-WAP). Raw sequence detailed metadata were submitted NCBI (BioProject PRJNA757291) it became available. Our successfully detected onset new BA.2, BA.2.12, BA.4.6, BA.5 observed population. Notably, Omicron sub-variants identified approximately week ahead publicly available clinical MD ZIP-code level. Variation quality metrics paralleled rise fall BA waves, underscoring impact viral load quality. Regular updates estimated proportions made FDA-CFSAN “Wastewater Surveillance Variants” website. In contrast median 28-day turnaround samples, lead via remarkably swift, accomplished mere 57 hours this specific exercise. processing, sequencing, methods empowered swift accurate trends community, offering insights health decision-making.

Language: Английский

Citations

0
Harnessing Methods, Data Analysis, and Near-Real-Time Wastewater Monitoring for Enhanced Public Health Response Using High Throughput Sequencing DOI
Padmini Ramachandran,

Tunc Kayikcioglu,

Tamara Walsky

et al.

Published: Jan. 1, 2024

Language: Английский

Citations

0
Detection and quantification of hepatitis A virus titers from wastewater in South Africa and comparison with clinical data from the National Surveillance Database DOI Creative Commons
Kathleen Subramoney, Sipho Gwala, Emmanuel Phalane

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Abstract Wastewater surveillance is useful for monitoring the prevalence of hepatitis A virus (HAV). We developed and optimized HAV detection quantification methods wastewater samples, applied them to samples collected through a national program. Previously identified 5’-untranslated region-targeting primers probes were used develop assay. Serial dilutions HAV-positive clinical validate determine limits (LOQ). Retrospective testing weekly SARS-CoV-2 program at 26 sites in Gauteng (August 2021 March 2024) undertaken using ultrafiltration-based concentration, nucleic acids extracted KingFisher Flex purification system with isolation kit. digital PCR assay was (as genome copies/μL). Clinical data from Surveillance Database Warehouse National Health Laboratory Service compared data, epidemiological week-wise district-wise, correlations between datasets. Based on validation results, one partition (dPCR) platform equivalent an LOQ 0.4 copies/μL. In total, 2013 tested, which 349 positive (17.3%), wherein majority (304, 87.1%) had lowest concentration (2.0-2.7 gc/μL, 1-5 partitions), followed by 20 (5.7%) concentrations 2.8-3.0 gc/μL (6-10 partitions). detected 17.1% (241/1170) 26.1% correlation anti-HAV IgM detected. successfully dPCR method detect quantify determined its LOQ. Further analysis required compare facilitate appropriate interpretation results.

Language: Английский

Citations

0